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Do you ever watch any of those reality cooking shows like Hells Kitchen or Top Chef? There are some really good chefs out there who are complete morons. Kind of like my friend Galen here.
Now if I hand in recipe, like this. He can follow the instructions. However, Galen is easily destructed. And if he wondered away to go find some nuts or flowers or other ingredients, he gets destructed and starts chasing puppies or reflections on the wall. So instead, to keep him from running away from the instructions, what I've done is I have a bunch of helpers who bring him the ingredients as he needs them. See, Galen look cook. "Nuts." This way everything comes to him and he doesn't get destructed.
Same thing happen in your cells when they are building proteins during the process of translation. Translation for those of you who don't know, is the taking of a sequence of RNA, called messenger RNA, and using that to instruct a ribosome on how to build the amino acid sequence that we call polypeptides or proteins.
Now I'm going to go through and discuss with you, how is that sequence or RNA translated into the actual amino acids. Then I'll get deeper into the process and I'll show you how does this whole thing begin with initiation. Then once we begin building our amino acid chain, how do we elongate that chain. Then finally, how doers this whole process come to an end.
So you know that the mRNA comes out of the nucleus as a long series of As, Us, Gs and Cs. So how does the sequence or basis gets translated into a sequence of amino acids. Well it turns out that it does it in groups of three, kind of like in Morse Code. In Morse Code you have these series of three dits or dots. So like the sequence dit-dit-dit means S or the sequence dot-dot-dot means O.
So you may be wondering why three bases at a time? Well remember with A-U-G and C, that's only four possibilities. And we need to represent 20 different possible amino acids, and so four is not just enough. If we use two bases at a time, that will be four times four, 16, which is close, but still not enough. So instead by using three, that gives us four times four times four. That's a total of 64, which is more than enough and that's actually is a good thing. This makes the generic code redundant.
And that redundancy means if there is a mutation of changing your DNA. There is a decent chance that it'll actually not have any effect on which amino acid is called for in any particular part of the protein.
So how do we translate these groups of three bases which are called Codons into amino acids? Let's take a look at the common Codon chart. You'll see all these things all over the place. In textbooks and if they ask you to do any translation on the AP Biology exam, they are going to give you this Codon chart. Nobody except for a few Biochemist freaks actually memorise it.
So, how does this work. Let's say for example you've got the Codon AGC. When you take a look, what's the first letter? The first letter when we take a look at this, is A. So I go here to where it says the first base, and I find the letter A. And I see all these have the first letter A. So let me highlight that in.
The second letter is G, so let's see. Across the top is the second letter, so G. Where's G? G is here. So I go and I'll use a different colour now. And now I know it's somewhere in here. So A, G and now for my last letter now I find the C, the third base. So AGC is Serine, Ser for short. They commonly use three letter abbreviations for the names of the amino acids because the full names are usually too long to memorise.
Let's take a look and see if you get this. What if I was doing say GCA? Go ahead, take a moment and see if you can figure it out, then I'll catch up to you. Let's see, G is the first letter, so that tells me it's G here. Then the second letter is C. C is down here and then A is last one. And I see it's Ala or Alanine for the long version. And you can see this is a good example of that redundancy.
Now there is a few particular Codons, these groups of three bases at a time, that you need to be very familiar with. First of those is AUG. That's how a ribosome, the organelle that actually does translation, knows where to begin. And so that is commonly called the START Codon. If we take a look here, let me go ahead and erase my high letter so you can see that. So here we see AUG, that code is for Methionine or Met for short.
So in every protein AUG is the START Codon. So every protein, the very first amino acid that's put in is Methionine. Now, that maybe later on clipped out after the protein is made if it's being put in the rough endoplasmic reticulum or the golgi apparatus for export. But again, AUG is the START codon and you got to burn that into your brain. Here is a simple way to remember it. In modern patterns, i.e. slang. How would you greet somebody that you've just met. You would say, "Hey you G, glad we met." So that's how you start a conversation.
How does the ribosome know when to end? That's what these guys are. UAA, UAG and UGA are known as the STOP Codons. All these others translate into particular amino acids. These translate into nothing. And when the ribosome hits this nothing it just stops waiting for something. And because there is nothing, it stops. So those are the STOP Codons.
Now you maybe saying, okay you know how this is done. You know how the Codons work but how is it actually translated. That requires the use of a special kind of RNA called tRNA or transfer RNA for the long name. So let's take a look at what a tRNA looks like. And that's this bizarre thing here and you can see it's a long sequence of RNA. Now you know that RNA is usually single stranded, but it can be double stranded for short sequences. That extra oxygen group that it has on it or OH group that it has on it, tends to make it unable to form double strands for long periods of time, but short sequences it can do.
Now the two key parts here, is this end here. This black end here carries what's called an anti Codon. You remember Chargaff's rules where A always joins to a U, if you're talking about RNA. G always joins to C. Well, if we've got the Codon AUG, then the anti-Codon will be UAC. So that's how this is able to match up to a Codon.
This end over here is the other key end. What this orange part here is, is it's an end that an enzyme else where in the cell recognises as the place to put in amino acid. So the tRNAs are properly called the transfer RNAs, because they transfer the amino acids from where they're being synthesized or where they're getting their food, to the ribosome where they can be used during translation or the building of the protein.
This would be really complicated for you to look at. So I'm going to simplify that a little bit when we're looking at our diagrams. So let's take a look at that.
So here we have our anti-Codon and here, this little hair thing, is the orange part. And my little pentagon or hexagon there, labelled Met, is our good friend Methionine. So this would be the tRNA that will be snatching up to AUG. It's got the correct anti-Codon and that's how we would start translation.
So now you know the messenger RNA codes for various amino acids, using these groups of three called Codons. Let's take a look at how this whole process begins. A scientist called the beginning of a process typically initiation. It's kind of like the 'initiation' process that you go through when you join a fraternity or a sorority. So how does initiation begin? Let's take a look.
Remember that messenger RNA has just come out of the nucleus, near its 5 prime end, you're going to have this structure here. This little orange blob here, come and find that 5 prime end, the beginning end of messenger RNA. Now what is this little thing here? That's the one half of a ribosome.
You should know that ribosomes have two parts. There is one part that's weak and then there is another part that's not so weak. Now scientists don't like using Scottish adjectives. So what they'll do is they'll call the small subunit. And then the other one that we'll take a look at in a little bit, the large subunit. Now near the 5 prime end is our buddy that START Codon AUG. So the small subunit will come along. And the small subunit has a groove in it that matches the shape of the sugar phosphate backbone of the messenger RNA. It will land on the mRNA and slide along it putting that mRNA into its groove until it stops with the AUG right there.
Now you'll also see the tRNA that matches up with its antiCodon, see A to U, U to A, G to C. Its anti-Codon match up to AUG, and it will bring with it that Met or Methionine as the first amino acid that we're going to put into our protein. Now what's this little red thing down there? That's a 'factor'. Specifically at this step since we're doing initiation. They call those initiation factors. And this is little trick about writing essays of any kind of molecular process, whether you're talking about protein synthesis or photosynthesis.
Scientists a lot of times when they first start studying these things they discover the main players. But then when they try to isolate it down to just those main players, they discover those other things that are involved that they haven't identified yet. They just clump those together as 'factors.'
So what they do is they just say, "We're doing initiation so there must be 'initiation' factors." So if you're writing an essay about protein synthesis, and you can't remember, toss in the name of the step that your in. Say initiation, say and this is helped by initiation factors. Later on, we're going to do elongation, that's helped by elongation factors. At the end we're going to do termination, termination factors. Remember on essays, you get points for being right, you don't loose points for being wrong. So if you happen to be right, you'll get a point. And if you're wrong, you don't loose anything. And remember, the readers are Biology teachers. Some are great at Botany some are great at Molecular Biology. You may trick a reader who's not all that great on say protein synthesis and they think, "Holy crap this kid knows more than I, I'll give him a point," because it sounds right.
What happens after the small subunits lands and we've got our tRNA there? The last step of initiation is when the large subunit comes along. So let's take a look at that. Here we see the large subunit coming in, now that we've got our small subunit, and our tRNA all lined up on this START Codon. The large subunit is this big blob here made up of RNA and proteins. The kind of RNA it's made of that's called rRNA. Not because it's a pirate but r for ribosomes, ribosome RNA.
Here we see it has three packets or sites in it. The E site, E there is in short for exit, because that's when we're done with tRNA they exit out that pocket. The P site is where we're going to be building our new protein and the A site is where new tRNAs arrive. When we're finally done with initiation, the whole initiation complex is going to look like this, with the large subunit landed on the START Codon. You can see that the large sub unit lands with that first tRNA sitting already in the P site. We've now finished initiation.
We've got the small subunit with and mRNA in its groove. We've got tRNA with it's appropriate anti-Codon matched up to the START Codon. And we've got its amino acid sitting right here on the P site, ready to be joined to whatever amino acid is brought by the next tRNA, which will come to its A site. So let's take a look in just a moment at how that happens during elongation.
So now that we have initiation completed, we're ready to go in, like I said, to elongation. So let's take a look at how that happens.
So during elongation we just make our amino acid chain or protein longer. So what happens is that, a tRNA comes along and matches up to the next Codon, that is sitting here in the A site. We have our start Codon, AUG here, the next Codon is CGA.
Now I'm too lazy to look up what CGA is. You can take a look at that in your Codon chart. So, because I'm too lazy, I just wrote amino acid number two. AA2 for short. So this tRNA carrying with it the correct amino acid that matches up to this Codon, it comes along. Now again, we've got one of our ready blobbed friends, that's the elongation factors. Since we're in elongation, we've got our helper molecules, elongation factor coming along. Now we've got our old tRNA sitting in the P site, our new one has arrived here in the A site. So now we're ready for the next step of elongation. And that's where we have to join these two amino acids together. This process is helped by an enzyme called Peptidyl transferase.
So we'll take a look at this now. And we'll see the Methionine is now joining to that second amino acid, that's what this black line here is. And just as a review for those of you who've been studying your proteins, what do we call the joint between one amino acid and the next? That's right, it's called a peptide bond. An old name for amino acids is peptides. We're building a multiple amino acid chain, or a polypeptide, with many of these peptide bonds.
But wait something is gone, "What is it?" See the little hair that used to be there? "You don't." This amino acid is still attached to it's tRNA, this one is not. Whenever you make bonds, you typically have to break bonds. So what happens is that the ribosome uses in it's special enzyme called Peptidyl Transferase, and breaks the bond between this tRNA and the amino acid or peptide, and transfers that bond to this amino acid. So now the ribosome is done with that first tRNA. It has no purpose for it. What's going to happen is that, the ribosome is going to shift and it's going to move down through three more bases, one more Codon.
So we're going to see the small subunit slide this way, and the large subunit slide along with it. And this movement is called translocation. For some reason, scientists think they are too cool to say they just move, so you'll see the term translocation appear a lot. Both in protein synthesis and it's a kind of chromosomal mutation just as a side note.
So we see first that tRNA which we have no more use for says, "Go away little boy." And it floats away. In comes the next tRNA. This of course is helped along by elongation factors. And it comes along and lands in this open Codon here in the A site. Why is the A site unoccupied? Remember that large subunits slid down bringing this tRNA, which used to be in A site, it stays still as the ribosome moves. And so now, our second tRNA it is in the P site. The first tRNA is going out the E site, and the new one is arriving in the A site. So E site, exit, P site growing protein, and A site is for new arrivals. And we just keep doing this over and over as the ribosomes down the mRNA adding in new amino acids as the tRNAs bring it in.
Now what happens to this guy? He goes off, finds the enzyme which recognises this anti-Codon and connects it with the correct amino acid. So we could see this same tRNA a little bit later bringing in another Methionine, if needed.
But how does this whole process end? That's called termination, which we'll address right now.
So how does termination happen? Well as the ribosome goes along it's adding in its amino acids. Eventually it reaches one of those STOP Codons. Remember, I talked about how there's no tRNA that matches up to that, here we see UAA in the A site. So the ribosomes are going on saying, "Oh! I need AUG again." And along comes the Methionine. And then it says, "I need a UAA." And there is no tRNA that matches up. So the ribosome sits are going, "I need a UAA." And it just stops waiting for non-existent tRNA to come along and bring this non-existent amino acid. Eventually, another helper molecule, a 'releasing factor' comes along and it says, "Stop, release." And that's what the ribosome does.
And what happens is that this last bond here gets broken up, and then everything just falls apart. And that's what we'll see here after the realising factor has caused the large subunit to release. It floats away, the small subunit also floats away. This last tRNA, its job done, floats away. And now our assemble protein chain, our amino acid sequence grouped together into this long sequence here, it floats away to be folded up and made up into a functional protein.
Alternately, it could be put in the rough endoplasmic reticulum, where perhaps it could be combined in other polypeptide chains or modified in some particular way. And maybe even sent off to the golgi apparatus for a preparation for a secretion from the cell. But that's it. We've gone through this whole thing, that's termination.
So that's translation, but I want to run through that one last time and I'm going to recreate it this time using myself as a ribosome. These cards here as the messengerRNA Codons.
I'll be having some assistance coming in bringing in some amino acids that I'm going to be using little coloured pieces of paper to represent the different amino acids. Now, I'm not dedicated enough to your education to saw myself in half to represent the two halves of the ribosomes. So you're just going to have to live with that.
Right here is my P site, here is my A site. Now you remember in initiation, what happens is the small subunit approaches and finds the START Codon. In this case represented by letters R-E-D which represents the colour of piece of paper red. Just like AUG, the START Codon represents the amino acid Methionine. So my small subunit comes along right here.
Now what else do I need? I need that first tRNA. How does it know to come here? Because it recognises the Codon RED using its anti-Codon. So, "RED." Moans the ribosome and along comes. Look it's the first tRNA, bringing with it its red amino acid. And it holds it right above the RED Codon. So I now look, notice she is in my P site. My A side is open, I'm ready to elongate. So my A side is where the new ones is going to arrive, so I go, "GREEN." And along comes green.
Now I'm going to use my enzyme Peptidyl transferase, so I have to break this bond here holding this red piece of paper on to the tRNA. And I make a peptide bond and she floats out my E site as I translocate or putting the blue Codon into my A site. He's now in my P site. Notice, he doesn't move. I do.
Okay, "Blue." And the tRNA that recognises with his anti-Codon, the BLUE Codon,e brings over the blue amino acid again, "Give me that." I break the bond, I make the bond. He goes out of my E site as I translocate down. Now I read the next Codon, "STOP." Now, there is no stop tRNA.
But the ribosome doesn't know that. It just poses because there is no tRNA that matches up to any of those STOP Codons, UAG, UGA or UAA. So I just sit there until finally a releasing factor, "STOP." Comes along and whacks me upside the back of my head. That breaks off our protein which may assemble into a protein channel or into an enzyme, or whatever. He floats away, I drift off and translation is done. That's it.
Now I really recommend that if you want to do really well on the AP Biology essay questions, that you spend some time either with your textbook or watch my episode on transcription. The process of actually making this messenger RNA. But if you get that down, you're going to do really well on one of the essays that they love to ask questions about. This topic reappears maybe every four years. So, get ready for it.